I am having a similar issue with manual invoices. The status is also set to “Pending Payment,” but I am not using PayPal Express Checkout option – I am using the PayPal powered by Braintree option only. In the regular checkout when a customer chooses a product from our shop and goes to checkout, the cc fields are shown and they can enter their information. However, if the customer clicks to pay the manual invoice from their orders on our site or from the emailed invoice the checkout page comes up and the “Pay by Credit Card” option shows but the fields for the cc information are missing.
My site is frostbitebox.com.